I just received this mail from the upstream author. Here's a rough
translation:

Here's a workaround. Maybe I find some time over christmas to do a real
fix.

----- Forwarded message from Ulrich Pfeifer <[EMAIL PROTECTED]> -----

From: Ulrich Pfeifer <[EMAIL PROTECTED]>
To: Florian Ragwitz <[EMAIL PROTECTED]>
Subject: Re: perlindex: libraries under /home/... get indexed as
 /usr//home/...
Date: Tue, 20 Dec 2005 11:04:10 +0100
User-Agent: Gnus/5.1007 (Gnus v5.10.7) Emacs/21.4 (gnu/linux)
X-Spam-Status: No, score=-2.6 required=5.0 tests=BAYES_00 autolearn=ham 
        version=3.0.2

Hallo,

    fr>     [EMAIL PROTECTED]:~$ perlindex ajax
    fr>     1  4.043 /home/dpchrist/share/perl/5.8.4/CGI/Ajax.pm
    fr>     2  0.067 /home/dpchrist/lib/perl/5.8.4/perllocal.pod

    fr>     Enter Number or 'q'> 1
    fr>     Running pod2man /usr//home/dpchrist/share/perl/5.8.4/CGI/Ajax.pm
    fr>     Can't open /usr//home/dpchrist/share/perl/5.8.4/CGI/Ajax.pm for read
    fr> ing: No such file or directory
    fr>     at /usr/bin/pod2man line 60

    fr> It looks like perlindex is adding '/usr/' to the front of modules it
    fr> finds under /home.

hier ist ein Workaround.  Vielleicht finde ich über Weihnachten die
Zeit für einen richtigen Fix.

--- orig/perlindex.PL
+++ mod/perlindex.PL
@@ -372,7 +372,7 @@
                     system 'man', $sect, $page;
                 } else {
                     my ($path) = ($selection =~ m:(\S+)$:);
-                    $path = $prefix.'/'.$path;
+                    $path = $prefix.'/'.$path unless -f $path;
                     print STDERR "Running pod2man $path\n";
                     system "pod2man --official $path | $nroff -man | $pager";
                 }

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